[gmx-users] Umbrella sampling with temperature and pressure coupling method problem

[Justin A. Lemkul]

chris.neale at utoronto.ca wrote:
> Use Langevin dynamics (the sd integrator) to control the temperature. 
> You are sure to get the correct ensemble that way and if you are doing 
> US then you can not extract dynamics anyway.
> 
> Hopefully somebody else can address the pressure coupling for you, but 
> probably you need to provide more information to get a useful answer there.
> 

The Berendsen barostat suffers from the same limitations as the thermostat - the 
pressure distribution does not produce a true NPT ensemble.

-Justin

> -- original message --
> 
> Dear all,
> 
>     I want to use umbrella sampling to calculate the PMF of the
> conformational transition of a protein. What temperature coupling method 
> and
> pressure coupling method should I use? Berendsen temperature coupling or
> Nose-Hoover temperature coupling? Or each one is OK?
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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